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| Status |
Public on Apr 26, 2021 |
| Title |
skin control3 10x scRNA-seq |
| Sample type |
SRA |
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| Source name |
control3
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| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
disease state: healthy
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| Extracted molecule |
total RNA |
| Extraction protocol |
Surgical tissue samples were obtained in accordance with the protocol approved by regional ethical review board. Patients with definite diagnosis of psoriasis were selected as donors, and the full-thickness skin of the lesion was excised surgically, and donors without systemic diseases undergoing surgery were selected as healthy controls, whose normal skin around the surgical margin was taken for the study. Subcutaneous fat and soft tissue were carefully scraped off using a scalpel. The full-thickness skin of the donor's trunk, about 1cm2 in size, was removed by surgery then transported in PBS buffer at 4 ℃ for less than 30 minutes from cutting to dissociation. Samples digestion was performed using the whole skin dissociation kit for human (130-101-540, Miltenyi Biotec). Enzymatic digestion was completed in 2h, followed by mechanical dissociation using gentleMacs Dissociator running the gentleMACS program h_skin_01. The red blood cell lysate buffer (C3702, Beyotime) was used to decompose the suspension on ice at 4 ℃ for 20 minutes. The total number of cells and the ratio of living cells were calculated by microscopy with 0.4% trypan blue (C0040, Solarbio) staining. Single cell suspension with a cell count more than 500,000 and alive cell rate more than 90% observed under a microscope can be tested in the next step.
Full protocol according to 10x genomics (V3.1)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x genomics (V3.1)
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| Data processing |
Count data were subsequently generated using CellRanger
10x demux pipeline was used to demultiplex the flowcells, and Fastq files were demultiplexed using mkfastq included in CellRanger.
Quality control of the processed expression matrix were performed by evaluating detected transcripts, detected counts, cell doublets, mito-ratio
Genome_build: GENCODE: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: HDF5 Loom file include raw counts, patient ID, UMAP, TSNE coordinates for each Sample
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| Submission date |
Nov 25, 2020 |
| Last update date |
Apr 26, 2021 |
| Contact name |
Yizhou Hu |
| E-mail(s) |
yizhou.hu@ki.se
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| Organization name |
Karolinska Institute
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| Street address |
C6 , Biomedicum Karolinska, Solnavägen 9,
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| City |
Solna |
| State/province |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE162183 |
Single cell transcriptional zonation of human psoriasis whole skin |
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| Relations |
| BioSample |
SAMN16915079 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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